SteinerNet

A web server for integrating 'omic' data to discover hidden components of response pathways

Nurcan Tuncbag, Scott McCallum, Shao-Shan Huang, Ernest Fraenkel

Research output: Contribution to journalArticle

Abstract

High-throughput technologies including transcriptional profiling, proteomics and reverse genetics screens provide detailed molecular descriptions of cellular responses to perturbations. However, it is difficult to integrate these diverse data to reconstruct biologically meaningful signaling networks. Previously, we have established a framework for integrating transcriptional, proteomic and interactome data by searching for the solution to the prize-collecting Steiner tree problem. Here, we present a web server, SteinerNet, to make this method available in a user-friendly format for a broad range of users with data from any species. At a minimum, a user only needs to provide a set of experimentally detected proteins and/or genes and the server will search for connections among these data from the provided interactomes for yeast, human, mouse, Drosophila melanogaster and Caenorhabditis elegans. More advanced users can upload their own interactome data as well. The server provides interactive visualization of the resulting optimal network and downloadable files detailing the analysis and results. We believe that SteinerNet will be useful for researchers who would like to integrate their high-throughput data for a specific condition or cellular response and to find biologically meaningful pathways. SteinerNet is accessible at http://fraenkel.mit.edu/steinernet.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume40
Issue numberW1
DOIs
StatePublished - Jul 1 2012

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Proteomics
Reverse Genetics
Caenorhabditis elegans
Drosophila melanogaster
Yeasts
Research Personnel
Technology
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

SteinerNet : A web server for integrating 'omic' data to discover hidden components of response pathways. / Tuncbag, Nurcan; McCallum, Scott; Huang, Shao-Shan; Fraenkel, Ernest.

In: Nucleic Acids Research, Vol. 40, No. W1, 01.07.2012.

Research output: Contribution to journalArticle

Tuncbag, Nurcan ; McCallum, Scott ; Huang, Shao-Shan ; Fraenkel, Ernest. / SteinerNet : A web server for integrating 'omic' data to discover hidden components of response pathways. In: Nucleic Acids Research. 2012 ; Vol. 40, No. W1.
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